That left him on eight-under for the tournament, one clear of 36-year-old Damien McGrane who used his experience of playing in windy weather back home in Ireland to card a battling 69.
Sweden's Henrik Stenson, defending champion, kept in touch in third place a further shot back after coming in early in the day with a 70, while Frenchman Thomas Levet pulled level with him thanks to a late 71.
"You can make a great swing, do everything right and get a gust and look like an idiot."
Seven players were a further stroke back on five-under including Spain's Sergio Garcia.
"I feel fine, pleased with anything in the red today," Woods said. "It was not a pretty day out there.
"We had a myriad of distractions out there and you had to be committed to what you're doing.
"You can make a great swing, do everything right and get a gust and look like an idiot. That's just the way it is."
The weather was in stark contrast to Thursday's placid, blue skies and warm sunshine when over 50 players finished their first rounds under par on at Emirates Golf Club.
Woods started the second round two strokes clear of the field after a commanding seven-under par 65 on Thursday and was looking for a repeat of his second round performance in his season-opener at the Buick Invitational in California last week.
Stenson and Els give chase
Stenson and Els were among those out early on day two, both set on keeping Woods in their sights, but they both dropped shots in the testing, early going as gusts of wind whipped up the desert sand and reduced visibility.
Playing together, they stuck to their tasks with Stenson getting to six-under, one behind Woods at that stage, after his round of 70 and Els finishing two strokes further back.
"It was really cold and windy this morning. It's very rare to have strong winds like this," Stenson, the Dubai resident said.
Several players made a run at Woods' lead in the afternoon after he opened with a bogey and at one stage both McGrane and South African Hennie Otto were ahead of the American by a stroke until he pulled ahead again at the finish.
Otto fell away with a double-bogey at the last, but McGrane held firm to set up a dream pairing with Woods on Saturday.
"I'm sure it's something that is going to be very different," the Irishman said.
"It's an experience I haven't had before playing with a player of his stature. I suppose there's nobody bigger in the game that's for sure.
"But he has his game and I have my game and I try to do the best with what I have."